Will of the people … South Sudan Civil Society Alliance workers call for a ceasefire during January peace talks in Juba. Photograph: Charles Atiki Lomodong/AFP/Getty

Two years after realising their dream of independence, the people of South Sudan are embroiled in yet another round of bloodshed over which they have little control. President Salva Kiir and former deputy Riek Machar, the country's two most senior political leaders, seem hellbent on mutual destruction in a winner-takes-all political power struggle.

There have been few positive developments in South Sudan since December 2013. But the African Union Commission's (AUC) recent appointment of an inquiry body that will investigate the widespread human rights violations should give hope to all Africans. Hope not only that the African Union stands by the commitment in its Constitutive Act to combat impunity and intervene to prevent mass atrocity crimes, but also that the people of South Sudan will finally be able to draw a line in the sand and begin to tackle the root causes of the recurring waves of violence they have suffered for decades.

By presenting a credible and objective account of events to date, the inquiry's report could help prevent those involved in the conflict from manipulating narratives to serve their own narrow political interests. The commission could also deter other African strongmen from inciting ethnic violence or committing gross human rights abuses by sending a message that this will come with serious legal consequences.

As the first commission of inquiry established by Nkosazana Dlamini-Zuma, the AUC chair, it will set important precedents for how the continent responds to mass atrocity crimes. This should be a commission that is truly independent, follows the facts wherever they lead, and publicly reports on its findings.

Tasked with recommending how to ensure the perpetrators of human rights violations should be held accountable, the commission will signal how the country can heal its ethnic divisions and build the democratic institutions crucial to its long-term stability. Completing this in the allotted three-month period will be a challenge, even for the five eminent African commissioners under the leadership of former Nigerian president Olusegun Obasanjo. But with the right specialist investigators, and experts in international law, sexual and gender-based violence, forensics and ballistics, it is not an insurmountable task. The AU can also draw on international support from the UN and others in its vital task.

However, the commission of inquiry alone is not the answer. It must conduct its work immediately, while evidence exists and witness testimony is fresh, but its recommendations cannot be implemented if the fighting persists. The UN security council – particularly the US and China, along with South Africa, the EU and Norway – must exert greater pressure on the warring parties to commit to inclusive political talks. Concerted diplomatic engagement by South Sudan's neighbours, particularly Ethiopia and Kenya, is also needed to ensure the conflict ends before it destabilises the region.

The AUC should heed the demands of South Sudan's people for transparent and accountable justice. Too often, African institutions, supported by the international community, have backed politically expedient deals between the men with guns to end deadly conflicts. There are examples from the early 1990s, when infighting among the Sudan People's Liberation Movement (SPLM) leadership tore ethnic communities apart. Those communities took part in the people-to-people peace process mediated by the church, but, because the SPLM never mustered the courage to own and confront the atrocities committed by its own leaders, the wounds were left to fester.

There should be no more blanket amnesties, quick political fixes or patching over the gaping holes in the country's governance. We should listen to the civil society voices from inside South Sudan that are appealing to the AU and the Intergovernmental Authority on Development to admit women, youth, religious leaders and NGOs. Only an inclusive negotiation process will lead to the reforms necessary for lasting peace and national reconciliation. Otherwise, South Sudan risks irreparable damage to its social fabric, potentially threatening the viability of the state. The untold sacrifices made by the people of South Sudan must not be in vain. Now is the moment of truth for leaders on both sides of the conflict.

Dr Suliman Baldo is an expert in international human rights and transitional justice. He is executive director of Sudan Democracy First Group and was a member of the UN commission of inquiry on Ivory Coast in 2011.